25 research outputs found
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Complete chloroplast genome sequences of Drimys, Liriodendron, andPiper: Implications for the phylogeny of magnoliids and the evolution ofGC content
The magnoliids represent the largest basal angiosperm clade with four orders, 19 families and 8,500 species. Although several recent angiosperm molecular phylogenies have supported the monophyly of magnoliids and suggested relationships among the orders, the limited number of genes examined resulted in only weak support, and these issues remain controversial. Furthermore, considerable incongruence has resulted in phylogenies supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. This is one of the most important remaining issues concerning relationships among basal angiosperms. We sequenced the chloroplast genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other completed angiosperm chloroplast genomes to assess phylogenetic relationships among magnoliids. The Drimys and Piper chloroplast genomes are nearly identical in size at 160,606 and 160,624 bp, respectively. The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper). The gene order of both taxa is nearly identical to many other unrearranged angiosperm chloroplast genomes, including Calycanthus, the other published magnoliid genome. Comparisons of angiosperm chloroplast genomes indicate that GC content is not uniformly distributed across the genome. Overall GC content ranges from 34-39%, and coding regions have a substantially higher GC content than non-coding regions (both intergenic spacers and introns). Among protein-coding genes, GC content varies by codon position with 1st codon > 2nd codon > 3rd codon, and it varies by functional group with photosynthetic genes having the highest percentage and NADH genes the lowest. Across the genome, GC content is highest in the inverted repeat due to the presence of rRNA genes and lowest in the small single copy region where most NADH genes are located. Phylogenetic analyses using maximum parsimony and maximum likelihood methods were performed on DNA sequences of 61 protein-coding genes. Trees from both analyses provided strong support for the monophyly of magnoliids and two strongly supported groups were identified, the Canellales/Piperales and the Laurales/Magnoliales. The phylogenies also provided moderate to strong support for the basal position of Amborella, and a sister relationship of magnoliids to a clade that includes monocots and eudicots. The complete sequences of three magnoliid chloroplast genomes provide new data from the largest basal angiosperm clade. Evolutionary comparisons of these new genome sequences, combined with other published angiosperm genome, confirm that GC content is unevenly distributed across the genome by location, codon position, and functional group. Furthermore, phylogenetic analyses provide the strongest support so far for the hypothesis that the magnoliids are sister to a large clade that includes both monocots and eudicots
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Advances in the operation of the DIII-D neutral beam computer systems
The DIII-D neutral beam system routinely provides up to 20 MW of deuterium neutral beam heating in support of experiments on the DIII-D tokamak, and is a critical part of the DIII-D physics experimental program. The four computer systems previously used to control neutral beam operation and data acquisition were designed and implemented in the late 1970`s and used on DIII and DIII-D from 1981--1996. By comparison to modern standards, they had become expensive to maintain, slow and cumbersome, making it difficult to implement improvements. Most critical of all, they were not networked computers. During the 1997 experimental campaign, these systems were replaced with new Unix compliant hardware and, for the most part, commercially available software. This paper describes operational experience with the new neutral beam computer systems, and new advances made possible by using features not previously available. These include retention and access to historical data, an asynchronously fired ``rules`` base, and a relatively straightforward programming interface. Methods and principles for extending the availability of data beyond the scope of the operator consoles will be discussed
Characterization of the global network of optical magnetometers to search for exotic physics (GNOME)
The Global Network of Optical Magnetometers to search for Exotic physics (GNOME) is a network of geographically separated, time-synchronized, optically pumped atomic magnetometers that is being used to search for correlated transient signals heralding exotic physics. The GNOME is sensitive to nuclear- and electron-spin couplings to exotic fields from astrophysical sources such as compact dark-matter objects (for example, axion stars and domain walls). Properties of the GNOME sensors such as sensitivity, bandwidth, and noise characteristics are studied in the present work, and features of the network’s operation (e.g., data acquisition, format, storage, and diagnostics) are described. Characterization of the GNOME is a key prerequisite to searches for and identification of exotic physics signatures
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Diii-D Plasma Control Simulation Environment
OAK-B135 Many advanced have been made to the DIII-D plasma control simulation environment since the previously developed hardware-in-the-loop plasma shape simulation capability was reported. In the present paper they summarize the major improvements to this simulation environment, including, introduction of the non-linear plasma evolution code DINA. Comparisons with DIII-D experimental results are presented. Recent model developments in advanced neoclassical tearing mode (NTM) and resistive wall mode (RWM) control are presented
Characterization of the global network of optical magnetometers to search for exotic physics (GNOME)
The Global Network of Optical Magnetometers to search for Exotic physics (GNOME) is a network of geographically separated, time-synchronized, optically pumped atomic magnetometers that is being used to search for correlated transient signals heralding exotic physics. The GNOME is sensitive to nuclear- and electron-spin couplings to exotic fields from astrophysical sources such as compact dark-matter objects (for example, axion stars and domain walls). Properties of the GNOME sensors such as sensitivity, bandwidth, and noise characteristics are studied in the present work, and features of the network’s operation (e.g., data acquisition, format, storage, and diagnostics) are described. Characterization of the GNOME is a key prerequisite to searches for and identification of exotic physics signatures
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Complete chloroplast genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogeny of magnoliids and the evolution of GC content
Recommended from our members
Complete chloroplast genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogeny of magnoliids and the evolution of GC content
Recommended from our members
DIII-D Thomson Scattering Diagnostic Data Acquisition, Processing, and Analysis Software
One of the diagnostic systems critical to the success of the DIII-D tokamak experiment is the Thomson scattering diagnostic. This diagnostic is unique in that it measures local electron temperature and density: (1) at multiple locations within the tokamak plasma; and (2) at different times throughout the plasma duration. Thomson ''raw'' data are digitized signals of scattered light, measured at different times and locations, from the laser beam paths fired into the plasma. Real-time acquisition of this data is performed by specialized hardware. Once obtained, the raw data are processed into meaningful temperature and density values which can be analyzed for measurement quality. This paper will provide an overview of the entire Thomson scattering diagnostic software and will focus on the data acquisition, processing, and analysis software implementation. The software falls into three general categories: (1) Set-up and Control: Initializes and controls all Thomson hardware and software, synchronizes with other DIII-D computers, and invokes other Thomson software as appropriate. (2) Data Acquisition and Processing: Obtains raw measured data from memory and processes it into temperature and density values. (3) Analysis: Provides a graphical user interface in which to perform analysis and sophisticated plotting of analysis parameters
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An algorithm to provide real time neutral beam substitution in the DIII-D tokamak
A key component of the DIII-D tokamak fusion experiment is a flexible and easy to expand digital control system which actively controls a large number of parameters in real-time. These include plasma shape, position, density, and total stored energy. This system, known as the PCS (plasma control system), also has the ability to directly control auxiliary plasma heating systems, such as the 20 MW of neutral beams routinely used on DIII-D. This paper describes the implementation of a real-time algorithm allowing substitution of power from one neutral beam for another, given a fault in the originally scheduled beam. Previously, in the event of a fault in one of the neutral beams, the actual power profile for the shot might be deficient, resulting in a less useful or wasted shot. Using this new real-time algorithm, a stand by neutral beam may substitute within milliseconds for one which has faulted. Since single shots can have substantial value, this is an important advance to DIII-D`s capabilities and utilization. Detailed results are presented, along with a description not only of the algorithm but of the simulation setup required to prove the algorithm without the costs normally associated with using physics operations time